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- PDB-6j5s: Crystal structure of human HINT1 mutant complexing with AP5A -

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Basic information

Entry
Database: PDB / ID: 6j5s
TitleCrystal structure of human HINT1 mutant complexing with AP5A
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / NUCLEOTIDE BINDING / REGULATION OF TRANSCRIPTION / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling / protein kinase C binding / cytoskeleton / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / ETHANESULFONIC ACID / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsWang, J. / Fang, P. / Guo, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21778067 China
National Natural Science Foundation of China21778064 China
CitationJournal: Nat Commun / Year: 2019
Title: Second messenger Ap4A polymerizes target protein HINT1 to transduce signals in Fc epsilon RI-activated mast cells.
Authors: Yu, J. / Liu, Z. / Liang, Y. / Luo, F. / Zhang, J. / Tian, C. / Motzik, A. / Zheng, M. / Kang, J. / Zhong, G. / Liu, C. / Fang, P. / Guo, M. / Razin, E. / Wang, J.
History
DepositionJan 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine triad nucleotide-binding protein 1
B: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9414
Polymers27,9142
Non-polymers1,0262
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-15 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.664, 46.475, 64.107
Angle α, β, γ (deg.)90.000, 94.110, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-202-

ESA

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Components

#1: Protein Histidine triad nucleotide-binding protein 1 / Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting ...Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting protein 1 / PKCI-1


Mass: 13957.096 Da / Num. of mol.: 2 / Mutation: H114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Chemical ChemComp-ESA / ETHANESULFONIC ACID


Mass: 110.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: HEPES pH 7.5, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.02→50 Å / Num. obs: 115657 / % possible obs: 98.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.9
Reflection shellResolution: 1.02→1.04 Å / Rmerge(I) obs: 0.456 / Num. unique obs: 3824

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EQE

4eqe


Resolution: 1.02→32.421 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 17.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1751 5788 5.01 %
Rwork0.1616 109769 -
obs0.1623 115557 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.34 Å2 / Biso mean: 13.8294 Å2 / Biso min: 4.87 Å2
Refinement stepCycle: final / Resolution: 1.02→32.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 63 437 2254
Biso mean--16.6 26.43 -
Num. residues----229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0202-1.05660.26415490.275102291077892
1.0566-1.09890.2425670.2329109661153399
1.0989-1.1490.19825830.2011110081159199
1.149-1.20950.19275800.1848110641164499
1.2095-1.28530.17296260.1699109541158099
1.2853-1.38460.17275770.1655110691164699
1.3846-1.52390.17565870.1578110491163699
1.5239-1.74440.16075740.1507110301160499
1.7444-2.19770.1635690.1536110511162099
2.1977-32.43690.16595760.14431134911925100
Refinement TLS params.Method: refined / Origin x: 13.0595 Å / Origin y: 1.1721 Å / Origin z: 16.0833 Å
111213212223313233
T0.0469 Å20.0006 Å2-0.0009 Å2-0.0517 Å2-0.0013 Å2--0.0678 Å2
L0.1404 °20.0344 °20.022 °2-0.4386 °20.0295 °2--1.0571 °2
S0.0017 Å °0.0143 Å °-0.0107 Å °0.0212 Å °-0.0037 Å °0.0181 Å °0.0427 Å °-0.0332 Å °0.0004 Å °
Refinement TLS groupSelection details: all

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